Wow, I'm amazed that such a critical bug hasn't been fixed - and bounties are required to get it done! Ignoring command line options and filter chains seems like a huge, mega blocker deal for ffmpeg/ffserver.

Fixed in d1e8d4b055bd9a79baa15ca80d9a1476d2a8ccdb
You can override ffservers input stuff with ffmpeg -override_ffserver and then specify all the map stuff to ffmpeg.
Also ffserver really is a community project with no single leader or core team behind it so instead of complaining its much more effective if you guys try to fix issues yourselfs and submit patches (that really applies to all the ffserver issues not so much this one now)